This study presents the numerical results for the aerodynamic and electromagnetic performances of an S-duct caret intake. Using the multilevel fast multipole method (MLFMM) to solve Maxwell equations, the current on the intake surface is calculated, and the radar cross-section (RCS) is analyzed. Moreover, the intake flow field is numerically investigated using the SST k–ω turbulence model to solve the Reynolds-averaged Navier–Stokes equations. Compared to a straight intake, for an S-duct caret intake, the average RCS is lower by 7.65 dB, and the maximum RCS difference value caused by the blade rotation is lower by 6.75 dB. However, the flow capacity deteriorates when the total pressure recovery coefficient decreases by 0.004. Based on the analysis of the aerodynamic and electromagnetic characteristics of different intakes, a double S-duct intake is designed. Compared to a traditional S-duct intake, for the novel intake after model parameter modification, the average RCS is lower by 0.05 dB, and the total pressure distortion (TPD) is lower by 0.18. The analysis of the effects of different boundary-layer bleed systems shows that the symmetrical layout adversely affects the aerodynamic and electromagnetic performances of the S-duct intake, but the unilateral partial layout is beneficial, whose TPD is lower by 0.04 and average RCS is higher by −2.17 dB compared to a straight intake.